Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models

By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice.

Extension of sound field reconstruction based on element radiation superposition method in a sparsity framework

Nearfield acoustic holography(NAH)is a powerful tool for realizing source identification and sound field reconstruction.The wave superposition(WS)-based NAH is appropriate for the spatially extended sources and does not require the complex numerical integrals.Equivalent source method(ESM),as a classical WS approach,is widely used due to its simplicity and efficiency.In the ESM,a virtual source surface is introduced,on which the virtual point sources are taken as the assumed sources,and an optimal retreat distance needs to be considered.A newly proposed WS-based approach,the element radiation superposition method(ERSM),uses piston surface source as the assumed source with no need to choose a virtual source surface.To satisfy the application conditions of piston pressure formula,the sizes of pistons are assumed to be as small as possible,which results in a large number of pistons and sampling points.In this paper,transfer matrix modes(TMMs),which are composed of the singular vectors of the vibro-acoustic transfer matrix,are used as the sparse basis of piston normal velocities.Then,the compressive ERSM based on TMMs is proposed.Compared with the conventional ERSM,the proposed method maintains a good pressure reconstruction when the number of sampling points and pistons are both reduced.Besides,the proposed method is compared with the compressive ESM in a mathematical sense.Both simulations and experiments for a rectangular plate demonstrate the advantage of the proposed method over the existing methods.

High-Field-Strength Elements in Mafic Volcanics from North China Craton: Implications for Archean-Proterozoic Boundary and Source Composition

Archean to Cenozoic mafic volcanic rocks from the North China craton are studied. They show Archean Proterozoic (Ar Pt) boundary and geochemical anomalies in Cenozoic basalts. Proterozoic mafic volcanics are enriched in most of the high field strength elements (HFSE) compared with Archean ones. Nb, Ta and Th show a distinct sequence of incompatibility in Archean and Proterozoic. The Cenozoic basalts are enriched in HFSE and Ni and their REEs are strongly differentiated with positive Eu anomalies ( δ (Eu)=1.14). The Ar Pt boundary could be related to change in oxygen fugacity and requires an increasing importance of enriched mantle source. The geochemistry of Cenozoic basalts implies a mantle source similar to OIB. Residuum from subducting partial melting of old basaltic oceanic crust and continental crust is likely to contribute to the formation of the enriched mantle.

Stress-corrosion coupled damage localization induced by secondary phases in bio-degradable Mg alloys:phase-field modeling

In this study,a phase-field scheme that rigorously obeys conservation laws and irreversible thermodynamics is developed for modeling stress-corrosion coupled damage(SCCD).The coupling constitutive relationships of the deformation,phase-field damage,mass transfer,and electrostatic field are derived from the entropy inequality.The SCCD localization induced by secondary phases in Mg is numerically simulated using the implicit iterative algorithm of the self-defined finite elements.The quantitative evaluation of the SCCD of a C-ring is in good agreement with the experimental results.To capture the damage localization,a micro-galvanic corrosion domain is defined,and the buffering effect on charge migration is explored.Three cases are investigated to reveal the effect of localization on corrosion acceleration and provide guidance for the design for resistance to SCCD at the crystal scale.

SIMULATION OF THE MAGNETIZATION REVERSAL PROCESS OF RECTANGLE-SHAPED NiFe FILM ELEMENTS UNDER AN ORTHOGONAL MAGNETIC FIELD

The magnetization reversal process of nano-size rectangle-shaped NiFe film elements with different aspect ratios have been investigated under the orthogonally applied magnetic fields by micromagnetic simulation. Different magnetization reversal modes can appear depending on whether the bias field is applied or not. When there is no bias field, double “C” state is the initial reversal state. However, when there is a bias field, “S” state is the starting mode. The larger the aspect ratio is, the larger the switching field is. But, when the aspect ratio is larger than 3, the increase of the switching field ceases. These results can provide useful information to the application of the patterned NiFe film with rectangular elements.

Vertical variation of trace elements and its relation to the water-bearing capacity of Ordovician strata,in Datun coal field

We tested for fourteen trace elements in samples collected from the Ordovician strata in Datun coal field.The vertical concentration variation of these trace elements is reported.The relationship of the variation to the water-bearing capacity of the Ordovician strata is discussed.The minimum concentration of eleven(of 14 total) trace elements appears in the lower Majiagou formation.The maximum concentrations mainly appear in the Badou and Jiawang formations:eight maxima are located in Badou and four more are in Jiawang.The study of karst development and the water-bearing capacity of Ordovician strata shows that karst is well developed in the Majiagou formation and there is a consequent high water-bearing capacity in this formation:Badou and Jiawang formations are contrary to this situation.The results illustrate that the minimum concentrations of most trace elements within certain Ordovician formations can be taken as strong evidence for the existence of a well developed karst and a high water-bearing capacity.

STUDY ON THE FRACTAL CHARACTER OF MAGNETIC ANOMALY FIELDS AND THE DELINEATION OF TECTONIC ELEMENTS IN THE SOUTH CHINA SEA

This is a quantitative method for studying the fractal character of magnetic anornaly fields and delineating tectonic elements using fractal theory . For an area with different geological and geophysical features , the definition of Hausdorff dimension is used to calculate the fractal dimension of the area’s magnetic field , then delineate geological tectonic elements by comparing this value . Use of 1978- 1986 geophysical survey data in this method applied to the South China Sea yielded three first grade tectonic elements and nine second grade ones , in six of which subsecond grade elernents were found.

Theoretical Analysis and Experimental Verification on Flow Field of Piezoelectric Pump with Unsymmetrical Slopes Element

Regular valveless piezoelectric pumps have rectifying elements outside their chambers to produce net flow. These rectifying elements outside the chamber will increase the overall volume of the pump and prevent its minimization. Valveless piezoelectric pump with unsymmetrical slopes elements（USE）, proposed in this paper, differs from other valveless pumps in that it is easy to be minimized by developing the chamber bottom as such a rectifying element. In this research, the working principle of the proposed pump was analyzed first. Numerical models were thereby established and numerical simulation was conducted to the chamber flow field with the method of time-dependent velocity. The effects of the USEs on the flow field in the chamber were shown clearly in simulation. And the particular feature of flow field in the chamber was discovered. It behaves a complex flow field, in which strong turbulent occurs companying a lot of vortexes in different directions and different sizes. This feature is just opposite to what regular piezoelectric pumps expect： a moderate flow field. The turbulent flow could be used to have different liquids stirred and well mixed in the chamber to produce homogeneous solution, emulsion or turbid liquid. Meanwhile, numerical simulation also presents the effect of the angles difference of the two slopes upon the flow field, and upon the flow rate of the pump, which fits to the theoretical analysis. Experiments with the proposed pump were also conducted to verify the numerical results. In these experiments, six USEs with different slope angles were used for efficiency tests, which proved the validity and reliability of the numerical analysis. The data obtained from numerical analysis agree well with that from the experiments. The errors ranged from 4.4% to 14.8% with their weighted average error being 9.7%.

COUPLED SIMULATION OF 3D ELECTRO-MAGNETO-FLOW FIELD IN HALL-HEROULT CELLS USING FINITE ELEMENT METHOD

Two full 3D steady mathematical models are developed by finite element method （FEM） to calcalate coupled physics fields. the electro-magnetic model is built and solved first and so is the fluid motion model with the acquired electromagnetic force as source body forces in Navier-Stokes equations. Effects caused by the ferromagnetic shell, busbar system around, and open boundary problem as well as inside induced current were considered in terms of the magnetic field. Furthermore, a new modeling method is found to set up solid models and then mesh them entirely with so-called structuralized grids, namely hex-mesh. Examples of 75kA prebaked cell with two kinds of busbar arrangements are presented. Results agree with those disclosed in the literature and confirm that the coupled simulation is valid. It is also concluded that the usage of these models facilitates the consistent analysis of the electric field to magnetic field and then flow motion to the greater extent, local distributions of current density and magnetic flux density are very much dependent on the cell structure, the steel shell is a shield to reduce the magnetic field and flow pattern is two dimensional in the main body of the metal pad.

Finite Element Numerical Simulation and PIV Measurement of Flow Field inside Metering-in Spool Valve

The finite element method （FEM） and particle image velocimetry （PIV） technique are utilized to get the flow field along the inlet passage, the chamber, the metering port and the outlet passage of spool valve at three different valve openings. For FEM numerical simulation, the stream function ψ-vorticity ω forms of continuity and Navier-Stokes equations are employed and FEM is applied to discrete the equations. Homemade simulation codes are executed to compute the values of stream function and vorticity at each node in the flow domain, then according to the correlation between stream function and velocity components, the velocity vectors of the whole field are calculated. For PIV experiment, pulse Nd： YAG laser is exploited to generate laser beam, cylindrical and spherical lenses are combined each other to produce 1.0 mm thickness laser sheet to illuminate the object plane, Polystyrene spherical particle with diameter of 30-50 μm is seeded in the fluid as a tracing particles, Kodak ES 1.0 CCD camera is employed to capture the images of interested, the images are processed with fast Fourier transform （FFT） cross-correlation algorithm and the processing results is displayed. Both results of numerical simulation and PIV experimental show that there are three main areas in the spool valve where vortex is formed. Numerical results also indicate that the valve opening have some effects on the flow structure of the valve. The investigation is helpful for qualitatively analyzing the energy loss, noise generating, steady state flow forces and even designing the geometry structure and flow passage.

STRESS FIELD ANALYSIS OF EXTRA-HEIGHT FORGING DIE USING FINITE ELEMENT METHOD

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3-D finite element modeling for evolution of stress field and interaction among strong earthquakes in Sichuan-Yunnan region

Based on the latest achievement about activities of geological structure, a 3-D finite-element model containing four layers of upper crust, lower crust (two layers) and upper mantle is established in the paper. By repeated tests and revisions, the boundary conditions of the model are determined. And then the background stress field, the stress field caused by fault creep and the stress field triggered by strong earthquake in Sichuan-Yunnan region, as well as their dynamic variations are calculated. The results indicate that the latter earthquake often occurs in the area with positive Coulomb rupture stress change associated with the former one, the former earthquake has a triggering effect on the latter one to a certain extent, and strong earthquake often occur in groups under the background of high stress, which is of great significance for distinguishing seismic anomalies, as well as for improving the level of earthquake prediction.

Neumann stochastic finite element method for calculating temperature field of frozen soil based on random field theory

To study the effect of uncertain factors on the temperature field of frozen soil, we propose a method to calculate the spatial average variance from just the point variance based on the local average theory of random fields. We model the heat transfer coefficient and specific heat capacity as spatially random fields instead of traditional random variables. An analysis for calculating the random temperature field of seasonal frozen soil is suggested by the Neumann stochastic finite element method, and here we provide the computational formulae of mathematical expectation, variance and variable coefficient. As shown in the calculation flow chart, the stochastic finite element calculation program for solving the random temperature field, as compiled by Matrix Laboratory （MATLAB） sottware, can directly output the statistical results of the temperature field of frozen soil. An example is presented to demonstrate the random effects from random field parameters, and the feasibility of the proposed approach is proven by compar- ing these results with the results derived when the random parameters are only modeled as random variables. The results show that the Neumann stochastic finite element method can efficiently solve the problem of random temperature fields of frozen soil based on random field theory, and it can reduce the variability of calculation results when the random parameters are modeled as spatial- ly random fields.

Finite element analysis of temperature field during multi-layer multi-pass weld-based rapid prototyping

During weld-bused rapid prototyping, the component experiences complex thermal process. In this paper, the temperature field evolution, thermal cycle characteristics, and temperature gradients of multi-layer multi-puss weld-based rapid prototyping are investigated using three-dimensional finite element models presented. The single-puss weld-bused rapid prototyping experiment is carried out. Thermal cycles calculated agree with experimental measurements. Furthermore, simulated results indicate that there exist the pre-heating effect of the fore layer and the post-heating effect of the rear layer in the multi-layer multi-pass weld-based rapid prototyping. In the first layer, the heat accumulates obviously. After the first layer, the dimension increase of the high temperature region behind the molten pool is not obvious. The heat diffusion condition in the first layer is the best, the heat diffusion condition in the second layer is the worst, and the heat diffusion conditions in the higher layers improve gradually.

Simulation of near-fault bedrock strong ground-motion field by explicit finite element method

Based on presumed active fault and corresponding model, this paper predicted the near-fault ground motion filed of a scenario earthquake （Mw=6 3/4 ） in an active fault by the explicit finite element method in combination with the source time function with improved transmitting artificial boundary and with high-frequency vibration contained. The results indicate that the improved artificial boundary is stable in numerical computation and the predicted strong ground motion has a consistent characteristic with the observed motion.

Higher-Order Line Element Analysis of Potential Field with Slender Heterogeneities

Potential field due to line sources residing on slender heterogeneities is involved in various areas,such as heat conduction,potential flow,and electrostatics.Often dipolar line sources are either prescribed or induced due to close interaction with other objects.Its calculation requires a higher-order scheme to take into account the dipolar effect as well as net source effect.In the present work,we apply such a higher-order line element method to analyze the potential field with cylindrical slender heterogeneities.In a benchmark example of two parallel rods,we compare the line element solution with the boundary element solution to show the accuracy as a function in terms of rods distance.Furthermore,we use more complicated examples to demonstrate the capability of the line element technique.

Finite element simulation of three-dimensional temperature field in underwater welding

Mathematical models of three-dimensional temperature fields in underwater welding with moving heat sources are built. Double ellipsoid Gauss model is proposed as heat sources models. Several factors which affect the temperature fields of underwater welding are analyzed. Water has little influence on thermal efftciency. Water convection coefftcient varies with the temperature difference between the water and the workpiece , and water convection makes molten pool freeze quickly. With the increase of water depth, the dimensions of heat sources model should be reduced as arc shrinks. Finite element technology is used to solve mathematical models. ANSYS software is used as finite element tool, and ANSYS Parametric Design Language is used to develop subprograms for loading the moving heat sources and the various convection coefftcients. Experiment results show that computational results by using double ellipsoid Gauss heat sources model accord well with the experimental results.

Probabilistic stability analyses of undrained slopes by 3D random fields and finite element methods

A long slope consisting of spatially random soils is a common geographical feature. This paper examined the necessity of three-dimensional(3 D) analysis when dealing with slope with full randomness in soil properties. Although 3 D random finite element analysis can well reflect the spatial variability of soil properties, it is often time-consuming for probabilistic stability analysis. For this reason, we also examined the least advantageous(or most pessimistic) cross-section of the studied slope. The concept of"most pessimistic" refers to the minimal cross-sectional average of undrained shear strength. The selection of the most pessimistic section is achievable by simulating the undrained shear strength as a 3 D random field. Random finite element analysis results suggest that two-dimensional(2 D) plane strain analysis based the most pessimistic cross-section generally provides a more conservative result than the corresponding full 3 D analysis. The level of conservativeness is around 15% on average. This result may have engineering implications for slope design where computationally tractable 2 D analyses based on the procedure proposed in this study could ensure conservative results.

Rock-soil slope stability analysis by two-phase random media and finite elements

To investigate the strong random nature of the geometric interfaces between soil and rock, a rock-soil slope is considered as a two-phase random medium. A nonlinear translation of a Gaussian field is utilized to simulate the two-phase random media, such that the soil(or rock) volume fraction and the inclination of the soil layer can be examined. The finite element method with random media incorporated as the material properties is used to determine the factor of safety of the rock-soil slope. Monte-Carlo simulations are used to estimate the statistical characteristics of the factor of safety. The failure mode of the rock-soil slope is examined by observing the maximum principal plastic strain at incipient slope failure. It is found that the critical surface of a rock-soil slope is fairly irregular, and it significantly differs from that of a pure soil slope. The factor of safety is sensitive to the soil volume faction, but it is predictable. The average factor of safety could be well predicted by the weighted harmonic average between the strength of soil and rock; the prediction model is practical and simple. Parametric studies on the inclination of the soil layer demonstrate that the most instable scenario occurs when the slope angle is consistent with the inclination of the soil layer.

Application of Wavelet Finite Element Method to Simulation of the Temperature Field of Copier Paper

Simulation of the temperature field of copier paper in copier fusing is very important for improving the fusing property of reprography. The temperature field of copier paper varies with a high gradient when the copier paper is moving through the fusing rollers. By means of conventional shaft elements, the high gradient temperature variety causes the oscillation of the numerical solution. Based on the Daubechies scaling functions, a kind of wavelet based element is constructed for the above problem. The temperature field of the copier paper moving through the fusing rollers is simulated using the two methods. Comparison of the results shows the advantages of the wavelet finite element method, which provides a new method for improving the copier properties.